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- PDB-7lc7: Crystal structure of epoxyqueuosine reductase QueH in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7lc7
TitleCrystal structure of epoxyqueuosine reductase QueH in complex with GMP from Thermotoga maritima
ComponentsEpoxyqueuosine reductase QueH
KeywordsOXIDOREDUCTASE / Epoxyqueuosine Reductase / QueH / Iron-Sulfur Cluster / GMP / Queuosine / tRNA
Function / homology
Function and homology information


epoxyqueuosine reductase / epoxyqueuosine reductase activity / queuosine biosynthetic process / tRNA processing / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Epoxyqueuosine reductase QueH / Epoxyqueuosine reductase QueH
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / : / IRON/SULFUR CLUSTER / Epoxyqueuosine reductase QueH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLi, Q. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM70641 United States
CitationJournal: To Be Published
Title: The epoxyqueuosine reductase QueH in the biosynthesis of tRNA queuosine is a unique metalloenzyme
Authors: Li, Q. / Bruner, S.D.
History
DepositionJan 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epoxyqueuosine reductase QueH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3555
Polymers22,5491
Non-polymers8064
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-46 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.335, 104.783, 73.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Epoxyqueuosine reductase QueH / Queuosine biosynthesis protein QueH


Mass: 22548.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: queH, TM_0731 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WZJ0, epoxyqueuosine reductase

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Non-polymers , 5 types, 90 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris, pH 5.5, 200 mM lithium sulfate monohydrate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2018
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.576→47.53 Å / Num. obs: 27990 / % possible obs: 96.78 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.24 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07859 / Rpim(I) all: 0.03314 / Rrim(I) all: 0.08552 / Net I/σ(I): 13.25
Reflection shellResolution: 1.576→1.633 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.6747 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 2694 / CC1/2: 0.834 / CC star: 0.954 / Rpim(I) all: 0.2866 / Rrim(I) all: 0.7346 / % possible all: 94.29

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7LC5

7lc5


Resolution: 1.58→47.53 Å / SU ML: 0.1881 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 1429 5.11 %
Rwork0.1999 26546 -
obs0.2021 27975 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.83 Å2
Refinement stepCycle: LAST / Resolution: 1.58→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 34 86 1588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681537
X-RAY DIFFRACTIONf_angle_d0.90172074
X-RAY DIFFRACTIONf_chiral_restr0.0696217
X-RAY DIFFRACTIONf_plane_restr0.0044260
X-RAY DIFFRACTIONf_dihedral_angle_d10.9866911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.630.34961530.282539X-RAY DIFFRACTION94.29
1.63-1.70.27051410.2542551X-RAY DIFFRACTION95.29
1.7-1.780.28361400.23992619X-RAY DIFFRACTION95.5
1.78-1.870.21921430.21412586X-RAY DIFFRACTION96.33
1.87-1.990.24321470.19692630X-RAY DIFFRACTION96.73
1.99-2.140.27881420.19122641X-RAY DIFFRACTION96.8
2.14-2.350.21091360.19462683X-RAY DIFFRACTION97.75
2.35-2.70.22681210.19862719X-RAY DIFFRACTION97.83
2.7-3.40.23761510.19912726X-RAY DIFFRACTION98.53
3.4-47.530.24211550.18932852X-RAY DIFFRACTION98.59

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